flowcyto_data_preparation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Preparation of the FlowCytometry data:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load in CSV files of the different cell groups obtained from manual gating with FlowCytometry analysis software:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>321</td>\n",
       "      <td>316</td>\n",
       "      <td>260</td>\n",
       "      <td>216</td>\n",
       "      <td>285</td>\n",
       "      <td>194</td>\n",
       "      <td>557</td>\n",
       "      <td>734</td>\n",
       "      <td>809</td>\n",
       "      <td>272</td>\n",
       "      <td>378</td>\n",
       "      <td>390</td>\n",
       "      <td>663</td>\n",
       "      <td>510</td>\n",
       "      <td>664</td>\n",
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       "      <th>1</th>\n",
       "      <td>327</td>\n",
       "      <td>300</td>\n",
       "      <td>278</td>\n",
       "      <td>170</td>\n",
       "      <td>268</td>\n",
       "      <td>163</td>\n",
       "      <td>595</td>\n",
       "      <td>452</td>\n",
       "      <td>793</td>\n",
       "      <td>262</td>\n",
       "      <td>264</td>\n",
       "      <td>356</td>\n",
       "      <td>229</td>\n",
       "      <td>401</td>\n",
       "      <td>586</td>\n",
       "      <td>685</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>422</td>\n",
       "      <td>296</td>\n",
       "      <td>365</td>\n",
       "      <td>232</td>\n",
       "      <td>285</td>\n",
       "      <td>209</td>\n",
       "      <td>629</td>\n",
       "      <td>609</td>\n",
       "      <td>705</td>\n",
       "      <td>288</td>\n",
       "      <td>351</td>\n",
       "      <td>397</td>\n",
       "      <td>259</td>\n",
       "      <td>244</td>\n",
       "      <td>659</td>\n",
       "      <td>452</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>333</td>\n",
       "      <td>322</td>\n",
       "      <td>265</td>\n",
       "      <td>273</td>\n",
       "      <td>301</td>\n",
       "      <td>233</td>\n",
       "      <td>616</td>\n",
       "      <td>586</td>\n",
       "      <td>755</td>\n",
       "      <td>288</td>\n",
       "      <td>280</td>\n",
       "      <td>413</td>\n",
       "      <td>186</td>\n",
       "      <td>399</td>\n",
       "      <td>638</td>\n",
       "      <td>874</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>366</td>\n",
       "      <td>295</td>\n",
       "      <td>317</td>\n",
       "      <td>177</td>\n",
       "      <td>269</td>\n",
       "      <td>169</td>\n",
       "      <td>530</td>\n",
       "      <td>482</td>\n",
       "      <td>769</td>\n",
       "      <td>279</td>\n",
       "      <td>293</td>\n",
       "      <td>337</td>\n",
       "      <td>254</td>\n",
       "      <td>484</td>\n",
       "      <td>623</td>\n",
       "      <td>814</td>\n",
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      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    321    316    260    216    285    194                            557   \n",
       "1    327    300    278    170    268    163                            595   \n",
       "2    422    296    365    232    285    209                            629   \n",
       "3    333    322    265    273    301    233                            616   \n",
       "4    366    295    317    177    269    169                            530   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   734                                    809   \n",
       "1                   452                                    793   \n",
       "2                   609                                    705   \n",
       "3                   586                                    755   \n",
       "4                   482                                    769   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 272                   378   \n",
       "1                                 262                   264   \n",
       "2                                 288                   351   \n",
       "3                                 288                   280   \n",
       "4                                 279                   293   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            390                 663   \n",
       "1                            356                 229   \n",
       "2                            397                 259   \n",
       "3                            413                 186   \n",
       "4                            337                 254   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       510                    664                      205   \n",
       "1                       401                    586                      685   \n",
       "2                       244                    659                      452   \n",
       "3                       399                    638                      874   \n",
       "4                       484                    623                      814   \n",
       "\n",
       "   Time :: CD226  \n",
       "0              0  \n",
       "1              0  \n",
       "2              0  \n",
       "3              0  \n",
       "4              0  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#total combined file:\n",
    "total_df_ungrouped = pd.read_csv(\"data/export_compensated_total.csv\")\n",
    "\n",
    "#Total live cells:\n",
    "live_df_ungrouped = pd.read_csv(\"data/export_compensated_total_live.csv\")\n",
    "\n",
    "#CD4 subtypes:\n",
    "CD4_tcm_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD4_tcm.csv\")\n",
    "CD4_tem_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD4_tem.csv\")\n",
    "CD4_temra_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD4_temra.csv\")\n",
    "CD4_th0_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD4_th0.csv\")\n",
    "\n",
    "#CD8 subtypes:\n",
    "CD8_tcm_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD8_tcm.csv\")\n",
    "CD8_tem_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD8_tem.csv\")\n",
    "CD8_temra_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD8_temra.csv\")\n",
    "CD8_tc0_df_ungrouped = pd.read_csv(\"data/export_compensated_total_CD8_tc0.csv\")\n",
    "\n",
    "\n",
    "\n",
    "total_df_ungrouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total (6807432, 17)\n",
      "live (4767912, 17)\n",
      "CD4_tcm (472548, 17)\n",
      "CD4_tem (471606, 17)\n",
      "CD4_temra (129912, 17)\n",
      "CD4_th0 (913463, 17)\n",
      "CD8_tcm (27806, 17)\n",
      "CD8_tem (261363, 17)\n",
      "CD8_temra (254410, 17)\n",
      "CD8_tc0 (323249, 17)\n"
     ]
    }
   ],
   "source": [
    "print(\"total\",total_df_ungrouped.shape)\n",
    "print(\"live\", live_df_ungrouped.shape)\n",
    "\n",
    "print(\"CD4_tcm\", CD4_tcm_df_ungrouped.shape)\n",
    "print(\"CD4_tem\", CD4_tem_df_ungrouped.shape)\n",
    "print(\"CD4_temra\", CD4_temra_df_ungrouped.shape)\n",
    "print(\"CD4_th0\", CD4_th0_df_ungrouped.shape)\n",
    "print(\"CD8_tcm\", CD8_tcm_df_ungrouped.shape)\n",
    "print(\"CD8_tem\", CD8_tem_df_ungrouped.shape)\n",
    "print(\"CD8_temra\", CD8_temra_df_ungrouped.shape)\n",
    "print(\"CD8_tc0\", CD8_tc0_df_ungrouped.shape)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a dataframe with none CD4/CD8 live cells:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1913555, 17)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Remove none CD4/CD8 by concat and removing duplicates from the total live dataframe:\n",
    "onlylive_df = pd.concat([live_df_ungrouped, CD4_tcm_df_ungrouped, CD4_tem_df_ungrouped, CD4_temra_df_ungrouped,\n",
    "                    CD4_th0_df_ungrouped, CD8_tcm_df_ungrouped, CD8_tem_df_ungrouped,\n",
    "                    CD8_temra_df_ungrouped, CD8_tc0_df_ungrouped]).drop_duplicates(keep=False).reset_index(drop=True)\n",
    "onlylive_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1913555"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Validate if the correct number of cells was substracted from the live dataframe by comparing shape:\n",
    "4767912-(472548+471606+129912+913463+27806+261363+254410+323249)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create dataframe containing double cells and debris:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "rest_df = pd.concat([total_df_ungrouped, live_df_ungrouped]).drop_duplicates(keep=False).reset_index(drop=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "rest_df.to_csv(\"data/dead_debris_ungrouped.csv\", index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
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       "      <th>0</th>\n",
       "      <td>270</td>\n",
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       "      <td>301</td>\n",
       "      <td>316</td>\n",
       "      <td>244</td>\n",
       "      <td>211</td>\n",
       "      <td>386</td>\n",
       "      <td>724</td>\n",
       "      <td>340</td>\n",
       "      <td>295</td>\n",
       "      <td>426</td>\n",
       "      <td>254</td>\n",
       "      <td>503</td>\n",
       "      <td>270</td>\n",
       "      <td>867</td>\n",
       "      <td>0</td>\n",
       "      <td>debris</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>917</td>\n",
       "      <td>460</td>\n",
       "      <td>511</td>\n",
       "      <td>707</td>\n",
       "      <td>403</td>\n",
       "      <td>450</td>\n",
       "      <td>643</td>\n",
       "      <td>666</td>\n",
       "      <td>918</td>\n",
       "      <td>408</td>\n",
       "      <td>361</td>\n",
       "      <td>656</td>\n",
       "      <td>140</td>\n",
       "      <td>426</td>\n",
       "      <td>633</td>\n",
       "      <td>812</td>\n",
       "      <td>0</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>235</td>\n",
       "      <td>270</td>\n",
       "      <td>223</td>\n",
       "      <td>134</td>\n",
       "      <td>263</td>\n",
       "      <td>131</td>\n",
       "      <td>489</td>\n",
       "      <td>224</td>\n",
       "      <td>381</td>\n",
       "      <td>302</td>\n",
       "      <td>264</td>\n",
       "      <td>590</td>\n",
       "      <td>244</td>\n",
       "      <td>226</td>\n",
       "      <td>231</td>\n",
       "      <td>707</td>\n",
       "      <td>0</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>310</td>\n",
       "      <td>316</td>\n",
       "      <td>251</td>\n",
       "      <td>220</td>\n",
       "      <td>277</td>\n",
       "      <td>203</td>\n",
       "      <td>594</td>\n",
       "      <td>578</td>\n",
       "      <td>776</td>\n",
       "      <td>271</td>\n",
       "      <td>283</td>\n",
       "      <td>401</td>\n",
       "      <td>184</td>\n",
       "      <td>584</td>\n",
       "      <td>645</td>\n",
       "      <td>793</td>\n",
       "      <td>1</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>545</td>\n",
       "      <td>383</td>\n",
       "      <td>364</td>\n",
       "      <td>934</td>\n",
       "      <td>352</td>\n",
       "      <td>679</td>\n",
       "      <td>352</td>\n",
       "      <td>484</td>\n",
       "      <td>869</td>\n",
       "      <td>588</td>\n",
       "      <td>550</td>\n",
       "      <td>573</td>\n",
       "      <td>263</td>\n",
       "      <td>87</td>\n",
       "      <td>368</td>\n",
       "      <td>508</td>\n",
       "      <td>1</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    270    336    206    301    316    244                            211   \n",
       "1    917    460    511    707    403    450                            643   \n",
       "2    235    270    223    134    263    131                            489   \n",
       "3    310    316    251    220    277    203                            594   \n",
       "4    545    383    364    934    352    679                            352   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   386                                    724   \n",
       "1                   666                                    918   \n",
       "2                   224                                    381   \n",
       "3                   578                                    776   \n",
       "4                   484                                    869   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 340                   295   \n",
       "1                                 408                   361   \n",
       "2                                 302                   264   \n",
       "3                                 271                   283   \n",
       "4                                 588                   550   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            426                 254   \n",
       "1                            656                 140   \n",
       "2                            590                 244   \n",
       "3                            401                 184   \n",
       "4                            573                 263   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       503                    270                      867   \n",
       "1                       426                    633                      812   \n",
       "2                       226                    231                      707   \n",
       "3                       584                    645                      793   \n",
       "4                        87                    368                      508   \n",
       "\n",
       "   Time :: CD226   class  \n",
       "0              0  debris  \n",
       "1              0  debris  \n",
       "2              0  debris  \n",
       "3              1  debris  \n",
       "4              1  debris  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rest_df_grouped = rest_df.copy()\n",
    "rest_df_grouped[\"class\"] = \"debris\"\n",
    "rest_df_grouped.to_csv(\"data/rest_df_grouped.csv\", index = False)\n",
    "rest_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "onlylive_df.to_csv(\"data/onlylive_ungrouped.csv\", index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>436</td>\n",
       "      <td>310</td>\n",
       "      <td>359</td>\n",
       "      <td>330</td>\n",
       "      <td>291</td>\n",
       "      <td>290</td>\n",
       "      <td>240</td>\n",
       "      <td>240</td>\n",
       "      <td>756</td>\n",
       "      <td>279</td>\n",
       "      <td>529</td>\n",
       "      <td>465</td>\n",
       "      <td>191</td>\n",
       "      <td>278</td>\n",
       "      <td>236</td>\n",
       "      <td>458</td>\n",
       "      <td>0</td>\n",
       "      <td>none_live</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>397</td>\n",
       "      <td>290</td>\n",
       "      <td>351</td>\n",
       "      <td>139</td>\n",
       "      <td>277</td>\n",
       "      <td>128</td>\n",
       "      <td>232</td>\n",
       "      <td>303</td>\n",
       "      <td>709</td>\n",
       "      <td>257</td>\n",
       "      <td>279</td>\n",
       "      <td>364</td>\n",
       "      <td>171</td>\n",
       "      <td>164</td>\n",
       "      <td>241</td>\n",
       "      <td>913</td>\n",
       "      <td>1</td>\n",
       "      <td>none_live</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>357</td>\n",
       "      <td>286</td>\n",
       "      <td>320</td>\n",
       "      <td>153</td>\n",
       "      <td>275</td>\n",
       "      <td>143</td>\n",
       "      <td>166</td>\n",
       "      <td>367</td>\n",
       "      <td>722</td>\n",
       "      <td>282</td>\n",
       "      <td>391</td>\n",
       "      <td>368</td>\n",
       "      <td>439</td>\n",
       "      <td>286</td>\n",
       "      <td>256</td>\n",
       "      <td>792</td>\n",
       "      <td>1</td>\n",
       "      <td>none_live</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>344</td>\n",
       "      <td>281</td>\n",
       "      <td>313</td>\n",
       "      <td>126</td>\n",
       "      <td>275</td>\n",
       "      <td>118</td>\n",
       "      <td>222</td>\n",
       "      <td>437</td>\n",
       "      <td>788</td>\n",
       "      <td>291</td>\n",
       "      <td>300</td>\n",
       "      <td>336</td>\n",
       "      <td>423</td>\n",
       "      <td>217</td>\n",
       "      <td>513</td>\n",
       "      <td>467</td>\n",
       "      <td>1</td>\n",
       "      <td>none_live</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>333</td>\n",
       "      <td>290</td>\n",
       "      <td>294</td>\n",
       "      <td>127</td>\n",
       "      <td>271</td>\n",
       "      <td>121</td>\n",
       "      <td>203</td>\n",
       "      <td>293</td>\n",
       "      <td>823</td>\n",
       "      <td>268</td>\n",
       "      <td>417</td>\n",
       "      <td>400</td>\n",
       "      <td>438</td>\n",
       "      <td>236</td>\n",
       "      <td>241</td>\n",
       "      <td>736</td>\n",
       "      <td>1</td>\n",
       "      <td>none_live</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    436    310    359    330    291    290                            240   \n",
       "1    397    290    351    139    277    128                            232   \n",
       "2    357    286    320    153    275    143                            166   \n",
       "3    344    281    313    126    275    118                            222   \n",
       "4    333    290    294    127    271    121                            203   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   240                                    756   \n",
       "1                   303                                    709   \n",
       "2                   367                                    722   \n",
       "3                   437                                    788   \n",
       "4                   293                                    823   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 279                   529   \n",
       "1                                 257                   279   \n",
       "2                                 282                   391   \n",
       "3                                 291                   300   \n",
       "4                                 268                   417   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            465                 191   \n",
       "1                            364                 171   \n",
       "2                            368                 439   \n",
       "3                            336                 423   \n",
       "4                            400                 438   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       278                    236                      458   \n",
       "1                       164                    241                      913   \n",
       "2                       286                    256                      792   \n",
       "3                       217                    513                      467   \n",
       "4                       236                    241                      736   \n",
       "\n",
       "   Time :: CD226      class  \n",
       "0              0  none_live  \n",
       "1              1  none_live  \n",
       "2              1  none_live  \n",
       "3              1  none_live  \n",
       "4              1  none_live  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "onlylive_df_grouped = onlylive_df.copy()\n",
    "onlylive_df_grouped[\"class\"] = \"none_live\"\n",
    "onlylive_df_grouped.to_csv(\"data/onlylive_grouped.csv\", index = False)\n",
    "onlylive_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
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       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>321</td>\n",
       "      <td>316</td>\n",
       "      <td>260</td>\n",
       "      <td>216</td>\n",
       "      <td>285</td>\n",
       "      <td>194</td>\n",
       "      <td>557</td>\n",
       "      <td>734</td>\n",
       "      <td>809</td>\n",
       "      <td>272</td>\n",
       "      <td>378</td>\n",
       "      <td>390</td>\n",
       "      <td>663</td>\n",
       "      <td>510</td>\n",
       "      <td>664</td>\n",
       "      <td>205</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>335</td>\n",
       "      <td>288</td>\n",
       "      <td>298</td>\n",
       "      <td>138</td>\n",
       "      <td>274</td>\n",
       "      <td>129</td>\n",
       "      <td>486</td>\n",
       "      <td>487</td>\n",
       "      <td>807</td>\n",
       "      <td>258</td>\n",
       "      <td>277</td>\n",
       "      <td>307</td>\n",
       "      <td>236</td>\n",
       "      <td>395</td>\n",
       "      <td>523</td>\n",
       "      <td>626</td>\n",
       "      <td>1</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>336</td>\n",
       "      <td>304</td>\n",
       "      <td>283</td>\n",
       "      <td>174</td>\n",
       "      <td>270</td>\n",
       "      <td>165</td>\n",
       "      <td>591</td>\n",
       "      <td>609</td>\n",
       "      <td>806</td>\n",
       "      <td>232</td>\n",
       "      <td>317</td>\n",
       "      <td>389</td>\n",
       "      <td>611</td>\n",
       "      <td>421</td>\n",
       "      <td>500</td>\n",
       "      <td>249</td>\n",
       "      <td>3</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>295</td>\n",
       "      <td>276</td>\n",
       "      <td>274</td>\n",
       "      <td>83</td>\n",
       "      <td>263</td>\n",
       "      <td>81</td>\n",
       "      <td>519</td>\n",
       "      <td>557</td>\n",
       "      <td>638</td>\n",
       "      <td>259</td>\n",
       "      <td>250</td>\n",
       "      <td>282</td>\n",
       "      <td>254</td>\n",
       "      <td>492</td>\n",
       "      <td>466</td>\n",
       "      <td>638</td>\n",
       "      <td>4</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>307</td>\n",
       "      <td>293</td>\n",
       "      <td>268</td>\n",
       "      <td>161</td>\n",
       "      <td>275</td>\n",
       "      <td>150</td>\n",
       "      <td>575</td>\n",
       "      <td>575</td>\n",
       "      <td>792</td>\n",
       "      <td>289</td>\n",
       "      <td>273</td>\n",
       "      <td>386</td>\n",
       "      <td>189</td>\n",
       "      <td>405</td>\n",
       "      <td>583</td>\n",
       "      <td>561</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    321    316    260    216    285    194                            557   \n",
       "1    335    288    298    138    274    129                            486   \n",
       "2    336    304    283    174    270    165                            591   \n",
       "3    295    276    274     83    263     81                            519   \n",
       "4    307    293    268    161    275    150                            575   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   734                                    809   \n",
       "1                   487                                    807   \n",
       "2                   609                                    806   \n",
       "3                   557                                    638   \n",
       "4                   575                                    792   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 272                   378   \n",
       "1                                 258                   277   \n",
       "2                                 232                   317   \n",
       "3                                 259                   250   \n",
       "4                                 289                   273   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            390                 663   \n",
       "1                            307                 236   \n",
       "2                            389                 611   \n",
       "3                            282                 254   \n",
       "4                            386                 189   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       510                    664                      205   \n",
       "1                       395                    523                      626   \n",
       "2                       421                    500                      249   \n",
       "3                       492                    466                      638   \n",
       "4                       405                    583                      561   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0              0  CD4_tcm  \n",
       "1              1  CD4_tcm  \n",
       "2              3  CD4_tcm  \n",
       "3              4  CD4_tcm  \n",
       "4              5  CD4_tcm  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD4_tcm_df_grouped = CD4_tcm_df_ungrouped.copy()\n",
    "CD4_tcm_df_grouped[\"class\"] = \"CD4_tcm\"\n",
    "CD4_tcm_df_grouped.to_csv(\"data/CD4_tcm_grouped.csv\", index = False)\n",
    "CD4_tcm_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
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       "      <th>FSC-H</th>\n",
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       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
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       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>422</td>\n",
       "      <td>296</td>\n",
       "      <td>365</td>\n",
       "      <td>232</td>\n",
       "      <td>285</td>\n",
       "      <td>209</td>\n",
       "      <td>629</td>\n",
       "      <td>609</td>\n",
       "      <td>705</td>\n",
       "      <td>288</td>\n",
       "      <td>351</td>\n",
       "      <td>397</td>\n",
       "      <td>259</td>\n",
       "      <td>244</td>\n",
       "      <td>659</td>\n",
       "      <td>452</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>398</td>\n",
       "      <td>298</td>\n",
       "      <td>342</td>\n",
       "      <td>159</td>\n",
       "      <td>267</td>\n",
       "      <td>152</td>\n",
       "      <td>570</td>\n",
       "      <td>566</td>\n",
       "      <td>760</td>\n",
       "      <td>321</td>\n",
       "      <td>292</td>\n",
       "      <td>372</td>\n",
       "      <td>255</td>\n",
       "      <td>171</td>\n",
       "      <td>609</td>\n",
       "      <td>295</td>\n",
       "      <td>2</td>\n",
       "      <td>CD4_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>496</td>\n",
       "      <td>317</td>\n",
       "      <td>401</td>\n",
       "      <td>249</td>\n",
       "      <td>294</td>\n",
       "      <td>217</td>\n",
       "      <td>524</td>\n",
       "      <td>622</td>\n",
       "      <td>715</td>\n",
       "      <td>248</td>\n",
       "      <td>420</td>\n",
       "      <td>392</td>\n",
       "      <td>531</td>\n",
       "      <td>274</td>\n",
       "      <td>540</td>\n",
       "      <td>489</td>\n",
       "      <td>3</td>\n",
       "      <td>CD4_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>460</td>\n",
       "      <td>314</td>\n",
       "      <td>375</td>\n",
       "      <td>297</td>\n",
       "      <td>295</td>\n",
       "      <td>257</td>\n",
       "      <td>582</td>\n",
       "      <td>682</td>\n",
       "      <td>758</td>\n",
       "      <td>293</td>\n",
       "      <td>397</td>\n",
       "      <td>403</td>\n",
       "      <td>237</td>\n",
       "      <td>231</td>\n",
       "      <td>638</td>\n",
       "      <td>325</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>355</td>\n",
       "      <td>325</td>\n",
       "      <td>280</td>\n",
       "      <td>254</td>\n",
       "      <td>290</td>\n",
       "      <td>224</td>\n",
       "      <td>543</td>\n",
       "      <td>613</td>\n",
       "      <td>832</td>\n",
       "      <td>303</td>\n",
       "      <td>369</td>\n",
       "      <td>425</td>\n",
       "      <td>242</td>\n",
       "      <td>235</td>\n",
       "      <td>620</td>\n",
       "      <td>458</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_tem</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    422    296    365    232    285    209                            629   \n",
       "1    398    298    342    159    267    152                            570   \n",
       "2    496    317    401    249    294    217                            524   \n",
       "3    460    314    375    297    295    257                            582   \n",
       "4    355    325    280    254    290    224                            543   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   609                                    705   \n",
       "1                   566                                    760   \n",
       "2                   622                                    715   \n",
       "3                   682                                    758   \n",
       "4                   613                                    832   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 288                   351   \n",
       "1                                 321                   292   \n",
       "2                                 248                   420   \n",
       "3                                 293                   397   \n",
       "4                                 303                   369   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            397                 259   \n",
       "1                            372                 255   \n",
       "2                            392                 531   \n",
       "3                            403                 237   \n",
       "4                            425                 242   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       244                    659                      452   \n",
       "1                       171                    609                      295   \n",
       "2                       274                    540                      489   \n",
       "3                       231                    638                      325   \n",
       "4                       235                    620                      458   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0              0  CD4_tem  \n",
       "1              2  CD4_tem  \n",
       "2              3  CD4_tem  \n",
       "3              5  CD4_tem  \n",
       "4              5  CD4_tem  "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD4_tem_df_grouped = CD4_tem_df_ungrouped.copy()\n",
    "CD4_tem_df_grouped[\"class\"] = \"CD4_tem\"\n",
    "CD4_tem_df_grouped.to_csv(\"data/CD4_tem_grouped.csv\", index = False)\n",
    "CD4_tem_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>332</td>\n",
       "      <td>297</td>\n",
       "      <td>286</td>\n",
       "      <td>162</td>\n",
       "      <td>272</td>\n",
       "      <td>152</td>\n",
       "      <td>578</td>\n",
       "      <td>496</td>\n",
       "      <td>719</td>\n",
       "      <td>288</td>\n",
       "      <td>261</td>\n",
       "      <td>358</td>\n",
       "      <td>237</td>\n",
       "      <td>223</td>\n",
       "      <td>542</td>\n",
       "      <td>772</td>\n",
       "      <td>1</td>\n",
       "      <td>CD4_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>473</td>\n",
       "      <td>317</td>\n",
       "      <td>382</td>\n",
       "      <td>247</td>\n",
       "      <td>272</td>\n",
       "      <td>232</td>\n",
       "      <td>541</td>\n",
       "      <td>526</td>\n",
       "      <td>816</td>\n",
       "      <td>287</td>\n",
       "      <td>304</td>\n",
       "      <td>418</td>\n",
       "      <td>235</td>\n",
       "      <td>319</td>\n",
       "      <td>595</td>\n",
       "      <td>724</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>345</td>\n",
       "      <td>306</td>\n",
       "      <td>289</td>\n",
       "      <td>211</td>\n",
       "      <td>270</td>\n",
       "      <td>200</td>\n",
       "      <td>594</td>\n",
       "      <td>608</td>\n",
       "      <td>712</td>\n",
       "      <td>274</td>\n",
       "      <td>268</td>\n",
       "      <td>399</td>\n",
       "      <td>419</td>\n",
       "      <td>289</td>\n",
       "      <td>616</td>\n",
       "      <td>779</td>\n",
       "      <td>14</td>\n",
       "      <td>CD4_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>350</td>\n",
       "      <td>302</td>\n",
       "      <td>296</td>\n",
       "      <td>166</td>\n",
       "      <td>323</td>\n",
       "      <td>131</td>\n",
       "      <td>559</td>\n",
       "      <td>595</td>\n",
       "      <td>762</td>\n",
       "      <td>300</td>\n",
       "      <td>301</td>\n",
       "      <td>392</td>\n",
       "      <td>246</td>\n",
       "      <td>256</td>\n",
       "      <td>661</td>\n",
       "      <td>819</td>\n",
       "      <td>14</td>\n",
       "      <td>CD4_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>388</td>\n",
       "      <td>299</td>\n",
       "      <td>332</td>\n",
       "      <td>223</td>\n",
       "      <td>282</td>\n",
       "      <td>202</td>\n",
       "      <td>553</td>\n",
       "      <td>504</td>\n",
       "      <td>735</td>\n",
       "      <td>360</td>\n",
       "      <td>295</td>\n",
       "      <td>353</td>\n",
       "      <td>187</td>\n",
       "      <td>265</td>\n",
       "      <td>521</td>\n",
       "      <td>805</td>\n",
       "      <td>16</td>\n",
       "      <td>CD4_temra</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    332    297    286    162    272    152                            578   \n",
       "1    473    317    382    247    272    232                            541   \n",
       "2    345    306    289    211    270    200                            594   \n",
       "3    350    302    296    166    323    131                            559   \n",
       "4    388    299    332    223    282    202                            553   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   496                                    719   \n",
       "1                   526                                    816   \n",
       "2                   608                                    712   \n",
       "3                   595                                    762   \n",
       "4                   504                                    735   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 288                   261   \n",
       "1                                 287                   304   \n",
       "2                                 274                   268   \n",
       "3                                 300                   301   \n",
       "4                                 360                   295   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            358                 237   \n",
       "1                            418                 235   \n",
       "2                            399                 419   \n",
       "3                            392                 246   \n",
       "4                            353                 187   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       223                    542                      772   \n",
       "1                       319                    595                      724   \n",
       "2                       289                    616                      779   \n",
       "3                       256                    661                      819   \n",
       "4                       265                    521                      805   \n",
       "\n",
       "   Time :: CD226      class  \n",
       "0              1  CD4_temra  \n",
       "1              5  CD4_temra  \n",
       "2             14  CD4_temra  \n",
       "3             14  CD4_temra  \n",
       "4             16  CD4_temra  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD4_temra_df_grouped = CD4_temra_df_ungrouped.copy()\n",
    "CD4_temra_df_grouped[\"class\"] = \"CD4_temra\"\n",
    "CD4_temra_df_grouped.to_csv(\"data/CD4_temra_grouped.csv\", index = False)\n",
    "CD4_temra_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>327</td>\n",
       "      <td>300</td>\n",
       "      <td>278</td>\n",
       "      <td>170</td>\n",
       "      <td>268</td>\n",
       "      <td>163</td>\n",
       "      <td>595</td>\n",
       "      <td>452</td>\n",
       "      <td>793</td>\n",
       "      <td>262</td>\n",
       "      <td>264</td>\n",
       "      <td>356</td>\n",
       "      <td>229</td>\n",
       "      <td>401</td>\n",
       "      <td>586</td>\n",
       "      <td>685</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_th0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>333</td>\n",
       "      <td>322</td>\n",
       "      <td>265</td>\n",
       "      <td>273</td>\n",
       "      <td>301</td>\n",
       "      <td>233</td>\n",
       "      <td>616</td>\n",
       "      <td>586</td>\n",
       "      <td>755</td>\n",
       "      <td>288</td>\n",
       "      <td>280</td>\n",
       "      <td>413</td>\n",
       "      <td>186</td>\n",
       "      <td>399</td>\n",
       "      <td>638</td>\n",
       "      <td>874</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_th0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>366</td>\n",
       "      <td>295</td>\n",
       "      <td>317</td>\n",
       "      <td>177</td>\n",
       "      <td>269</td>\n",
       "      <td>169</td>\n",
       "      <td>530</td>\n",
       "      <td>482</td>\n",
       "      <td>769</td>\n",
       "      <td>279</td>\n",
       "      <td>293</td>\n",
       "      <td>337</td>\n",
       "      <td>254</td>\n",
       "      <td>484</td>\n",
       "      <td>623</td>\n",
       "      <td>814</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_th0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>460</td>\n",
       "      <td>319</td>\n",
       "      <td>370</td>\n",
       "      <td>245</td>\n",
       "      <td>286</td>\n",
       "      <td>219</td>\n",
       "      <td>606</td>\n",
       "      <td>642</td>\n",
       "      <td>713</td>\n",
       "      <td>273</td>\n",
       "      <td>289</td>\n",
       "      <td>423</td>\n",
       "      <td>150</td>\n",
       "      <td>546</td>\n",
       "      <td>709</td>\n",
       "      <td>882</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_th0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>388</td>\n",
       "      <td>327</td>\n",
       "      <td>304</td>\n",
       "      <td>235</td>\n",
       "      <td>297</td>\n",
       "      <td>203</td>\n",
       "      <td>510</td>\n",
       "      <td>565</td>\n",
       "      <td>747</td>\n",
       "      <td>283</td>\n",
       "      <td>289</td>\n",
       "      <td>421</td>\n",
       "      <td>119</td>\n",
       "      <td>405</td>\n",
       "      <td>649</td>\n",
       "      <td>864</td>\n",
       "      <td>1</td>\n",
       "      <td>CD4_th0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    327    300    278    170    268    163                            595   \n",
       "1    333    322    265    273    301    233                            616   \n",
       "2    366    295    317    177    269    169                            530   \n",
       "3    460    319    370    245    286    219                            606   \n",
       "4    388    327    304    235    297    203                            510   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   452                                    793   \n",
       "1                   586                                    755   \n",
       "2                   482                                    769   \n",
       "3                   642                                    713   \n",
       "4                   565                                    747   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 262                   264   \n",
       "1                                 288                   280   \n",
       "2                                 279                   293   \n",
       "3                                 273                   289   \n",
       "4                                 283                   289   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            356                 229   \n",
       "1                            413                 186   \n",
       "2                            337                 254   \n",
       "3                            423                 150   \n",
       "4                            421                 119   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       401                    586                      685   \n",
       "1                       399                    638                      874   \n",
       "2                       484                    623                      814   \n",
       "3                       546                    709                      882   \n",
       "4                       405                    649                      864   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0              0  CD4_th0  \n",
       "1              0  CD4_th0  \n",
       "2              0  CD4_th0  \n",
       "3              0  CD4_th0  \n",
       "4              1  CD4_th0  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD4_th0_df_grouped = CD4_th0_df_ungrouped.copy()\n",
    "CD4_th0_df_grouped[\"class\"] = \"CD4_th0\"\n",
    "CD4_th0_df_grouped.to_csv(\"data/CD4_th0_grouped.csv\", index = False)\n",
    "CD4_th0_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>325</td>\n",
       "      <td>278</td>\n",
       "      <td>299</td>\n",
       "      <td>83</td>\n",
       "      <td>261</td>\n",
       "      <td>81</td>\n",
       "      <td>84</td>\n",
       "      <td>627</td>\n",
       "      <td>703</td>\n",
       "      <td>456</td>\n",
       "      <td>285</td>\n",
       "      <td>327</td>\n",
       "      <td>244</td>\n",
       "      <td>376</td>\n",
       "      <td>431</td>\n",
       "      <td>286</td>\n",
       "      <td>65</td>\n",
       "      <td>CD8_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>453</td>\n",
       "      <td>330</td>\n",
       "      <td>351</td>\n",
       "      <td>277</td>\n",
       "      <td>294</td>\n",
       "      <td>241</td>\n",
       "      <td>152</td>\n",
       "      <td>590</td>\n",
       "      <td>807</td>\n",
       "      <td>493</td>\n",
       "      <td>459</td>\n",
       "      <td>441</td>\n",
       "      <td>531</td>\n",
       "      <td>399</td>\n",
       "      <td>638</td>\n",
       "      <td>391</td>\n",
       "      <td>86</td>\n",
       "      <td>CD8_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>383</td>\n",
       "      <td>304</td>\n",
       "      <td>322</td>\n",
       "      <td>192</td>\n",
       "      <td>277</td>\n",
       "      <td>178</td>\n",
       "      <td>114</td>\n",
       "      <td>654</td>\n",
       "      <td>697</td>\n",
       "      <td>594</td>\n",
       "      <td>292</td>\n",
       "      <td>375</td>\n",
       "      <td>200</td>\n",
       "      <td>574</td>\n",
       "      <td>630</td>\n",
       "      <td>612</td>\n",
       "      <td>160</td>\n",
       "      <td>CD8_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>330</td>\n",
       "      <td>281</td>\n",
       "      <td>300</td>\n",
       "      <td>110</td>\n",
       "      <td>266</td>\n",
       "      <td>106</td>\n",
       "      <td>128</td>\n",
       "      <td>580</td>\n",
       "      <td>782</td>\n",
       "      <td>482</td>\n",
       "      <td>275</td>\n",
       "      <td>346</td>\n",
       "      <td>230</td>\n",
       "      <td>513</td>\n",
       "      <td>556</td>\n",
       "      <td>534</td>\n",
       "      <td>218</td>\n",
       "      <td>CD8_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>311</td>\n",
       "      <td>293</td>\n",
       "      <td>271</td>\n",
       "      <td>144</td>\n",
       "      <td>283</td>\n",
       "      <td>130</td>\n",
       "      <td>140</td>\n",
       "      <td>602</td>\n",
       "      <td>786</td>\n",
       "      <td>651</td>\n",
       "      <td>275</td>\n",
       "      <td>382</td>\n",
       "      <td>181</td>\n",
       "      <td>443</td>\n",
       "      <td>521</td>\n",
       "      <td>684</td>\n",
       "      <td>222</td>\n",
       "      <td>CD8_tcm</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    325    278    299     83    261     81                             84   \n",
       "1    453    330    351    277    294    241                            152   \n",
       "2    383    304    322    192    277    178                            114   \n",
       "3    330    281    300    110    266    106                            128   \n",
       "4    311    293    271    144    283    130                            140   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   627                                    703   \n",
       "1                   590                                    807   \n",
       "2                   654                                    697   \n",
       "3                   580                                    782   \n",
       "4                   602                                    786   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 456                   285   \n",
       "1                                 493                   459   \n",
       "2                                 594                   292   \n",
       "3                                 482                   275   \n",
       "4                                 651                   275   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            327                 244   \n",
       "1                            441                 531   \n",
       "2                            375                 200   \n",
       "3                            346                 230   \n",
       "4                            382                 181   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       376                    431                      286   \n",
       "1                       399                    638                      391   \n",
       "2                       574                    630                      612   \n",
       "3                       513                    556                      534   \n",
       "4                       443                    521                      684   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0             65  CD8_tcm  \n",
       "1             86  CD8_tcm  \n",
       "2            160  CD8_tcm  \n",
       "3            218  CD8_tcm  \n",
       "4            222  CD8_tcm  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD8_tcm_df_grouped = CD8_tcm_df_ungrouped.copy()\n",
    "CD8_tcm_df_grouped[\"class\"] = \"CD8_tcm\"\n",
    "CD8_tcm_df_grouped.to_csv(\"data/CD8_tcm_grouped.csv\", index = False)\n",
    "CD8_tcm_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>483</td>\n",
       "      <td>327</td>\n",
       "      <td>378</td>\n",
       "      <td>306</td>\n",
       "      <td>292</td>\n",
       "      <td>268</td>\n",
       "      <td>145</td>\n",
       "      <td>525</td>\n",
       "      <td>850</td>\n",
       "      <td>622</td>\n",
       "      <td>410</td>\n",
       "      <td>440</td>\n",
       "      <td>450</td>\n",
       "      <td>179</td>\n",
       "      <td>616</td>\n",
       "      <td>641</td>\n",
       "      <td>1</td>\n",
       "      <td>CD8_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>315</td>\n",
       "      <td>285</td>\n",
       "      <td>283</td>\n",
       "      <td>162</td>\n",
       "      <td>275</td>\n",
       "      <td>151</td>\n",
       "      <td>229</td>\n",
       "      <td>463</td>\n",
       "      <td>637</td>\n",
       "      <td>575</td>\n",
       "      <td>273</td>\n",
       "      <td>339</td>\n",
       "      <td>269</td>\n",
       "      <td>162</td>\n",
       "      <td>246</td>\n",
       "      <td>637</td>\n",
       "      <td>2</td>\n",
       "      <td>CD8_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>378</td>\n",
       "      <td>286</td>\n",
       "      <td>339</td>\n",
       "      <td>144</td>\n",
       "      <td>277</td>\n",
       "      <td>133</td>\n",
       "      <td>234</td>\n",
       "      <td>439</td>\n",
       "      <td>808</td>\n",
       "      <td>560</td>\n",
       "      <td>371</td>\n",
       "      <td>377</td>\n",
       "      <td>181</td>\n",
       "      <td>175</td>\n",
       "      <td>269</td>\n",
       "      <td>651</td>\n",
       "      <td>2</td>\n",
       "      <td>CD8_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>328</td>\n",
       "      <td>276</td>\n",
       "      <td>304</td>\n",
       "      <td>122</td>\n",
       "      <td>264</td>\n",
       "      <td>118</td>\n",
       "      <td>223</td>\n",
       "      <td>554</td>\n",
       "      <td>689</td>\n",
       "      <td>491</td>\n",
       "      <td>274</td>\n",
       "      <td>314</td>\n",
       "      <td>431</td>\n",
       "      <td>266</td>\n",
       "      <td>301</td>\n",
       "      <td>642</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8_tem</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>408</td>\n",
       "      <td>281</td>\n",
       "      <td>371</td>\n",
       "      <td>225</td>\n",
       "      <td>283</td>\n",
       "      <td>204</td>\n",
       "      <td>251</td>\n",
       "      <td>405</td>\n",
       "      <td>936</td>\n",
       "      <td>535</td>\n",
       "      <td>436</td>\n",
       "      <td>412</td>\n",
       "      <td>245</td>\n",
       "      <td>242</td>\n",
       "      <td>283</td>\n",
       "      <td>662</td>\n",
       "      <td>11</td>\n",
       "      <td>CD8_tem</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    483    327    378    306    292    268                            145   \n",
       "1    315    285    283    162    275    151                            229   \n",
       "2    378    286    339    144    277    133                            234   \n",
       "3    328    276    304    122    264    118                            223   \n",
       "4    408    281    371    225    283    204                            251   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   525                                    850   \n",
       "1                   463                                    637   \n",
       "2                   439                                    808   \n",
       "3                   554                                    689   \n",
       "4                   405                                    936   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 622                   410   \n",
       "1                                 575                   273   \n",
       "2                                 560                   371   \n",
       "3                                 491                   274   \n",
       "4                                 535                   436   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            440                 450   \n",
       "1                            339                 269   \n",
       "2                            377                 181   \n",
       "3                            314                 431   \n",
       "4                            412                 245   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       179                    616                      641   \n",
       "1                       162                    246                      637   \n",
       "2                       175                    269                      651   \n",
       "3                       266                    301                      642   \n",
       "4                       242                    283                      662   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0              1  CD8_tem  \n",
       "1              2  CD8_tem  \n",
       "2              2  CD8_tem  \n",
       "3              8  CD8_tem  \n",
       "4             11  CD8_tem  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD8_tem_df_grouped = CD8_tem_df_ungrouped.copy()\n",
    "CD8_tem_df_grouped[\"class\"] = \"CD8_tem\"\n",
    "CD8_tem_df_grouped.to_csv(\"data/CD8_tem_grouped.csv\", index = False)\n",
    "CD8_tem_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>442</td>\n",
       "      <td>317</td>\n",
       "      <td>357</td>\n",
       "      <td>168</td>\n",
       "      <td>289</td>\n",
       "      <td>149</td>\n",
       "      <td>89</td>\n",
       "      <td>524</td>\n",
       "      <td>754</td>\n",
       "      <td>575</td>\n",
       "      <td>308</td>\n",
       "      <td>417</td>\n",
       "      <td>66</td>\n",
       "      <td>318</td>\n",
       "      <td>688</td>\n",
       "      <td>922</td>\n",
       "      <td>1</td>\n",
       "      <td>CD8_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>413</td>\n",
       "      <td>322</td>\n",
       "      <td>328</td>\n",
       "      <td>254</td>\n",
       "      <td>298</td>\n",
       "      <td>218</td>\n",
       "      <td>201</td>\n",
       "      <td>570</td>\n",
       "      <td>650</td>\n",
       "      <td>623</td>\n",
       "      <td>338</td>\n",
       "      <td>408</td>\n",
       "      <td>109</td>\n",
       "      <td>301</td>\n",
       "      <td>608</td>\n",
       "      <td>893</td>\n",
       "      <td>11</td>\n",
       "      <td>CD8_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>482</td>\n",
       "      <td>338</td>\n",
       "      <td>365</td>\n",
       "      <td>259</td>\n",
       "      <td>298</td>\n",
       "      <td>222</td>\n",
       "      <td>167</td>\n",
       "      <td>408</td>\n",
       "      <td>717</td>\n",
       "      <td>500</td>\n",
       "      <td>285</td>\n",
       "      <td>415</td>\n",
       "      <td>202</td>\n",
       "      <td>241</td>\n",
       "      <td>342</td>\n",
       "      <td>755</td>\n",
       "      <td>13</td>\n",
       "      <td>CD8_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>416</td>\n",
       "      <td>328</td>\n",
       "      <td>325</td>\n",
       "      <td>300</td>\n",
       "      <td>282</td>\n",
       "      <td>272</td>\n",
       "      <td>178</td>\n",
       "      <td>611</td>\n",
       "      <td>769</td>\n",
       "      <td>529</td>\n",
       "      <td>344</td>\n",
       "      <td>379</td>\n",
       "      <td>98</td>\n",
       "      <td>278</td>\n",
       "      <td>638</td>\n",
       "      <td>937</td>\n",
       "      <td>15</td>\n",
       "      <td>CD8_temra</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>322</td>\n",
       "      <td>281</td>\n",
       "      <td>293</td>\n",
       "      <td>141</td>\n",
       "      <td>266</td>\n",
       "      <td>136</td>\n",
       "      <td>188</td>\n",
       "      <td>457</td>\n",
       "      <td>579</td>\n",
       "      <td>572</td>\n",
       "      <td>252</td>\n",
       "      <td>309</td>\n",
       "      <td>454</td>\n",
       "      <td>167</td>\n",
       "      <td>232</td>\n",
       "      <td>782</td>\n",
       "      <td>17</td>\n",
       "      <td>CD8_temra</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    442    317    357    168    289    149                             89   \n",
       "1    413    322    328    254    298    218                            201   \n",
       "2    482    338    365    259    298    222                            167   \n",
       "3    416    328    325    300    282    272                            178   \n",
       "4    322    281    293    141    266    136                            188   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   524                                    754   \n",
       "1                   570                                    650   \n",
       "2                   408                                    717   \n",
       "3                   611                                    769   \n",
       "4                   457                                    579   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 575                   308   \n",
       "1                                 623                   338   \n",
       "2                                 500                   285   \n",
       "3                                 529                   344   \n",
       "4                                 572                   252   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            417                  66   \n",
       "1                            408                 109   \n",
       "2                            415                 202   \n",
       "3                            379                  98   \n",
       "4                            309                 454   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       318                    688                      922   \n",
       "1                       301                    608                      893   \n",
       "2                       241                    342                      755   \n",
       "3                       278                    638                      937   \n",
       "4                       167                    232                      782   \n",
       "\n",
       "   Time :: CD226      class  \n",
       "0              1  CD8_temra  \n",
       "1             11  CD8_temra  \n",
       "2             13  CD8_temra  \n",
       "3             15  CD8_temra  \n",
       "4             17  CD8_temra  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD8_temra_df_grouped = CD8_temra_df_ungrouped.copy()\n",
    "CD8_temra_df_grouped[\"class\"] = \"CD8_temra\"\n",
    "CD8_temra_df_grouped.to_csv(\"data/CD8_temra_grouped.csv\", index = False)\n",
    "CD8_temra_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>440</td>\n",
       "      <td>353</td>\n",
       "      <td>319</td>\n",
       "      <td>226</td>\n",
       "      <td>288</td>\n",
       "      <td>201</td>\n",
       "      <td>119</td>\n",
       "      <td>565</td>\n",
       "      <td>798</td>\n",
       "      <td>580</td>\n",
       "      <td>287</td>\n",
       "      <td>414</td>\n",
       "      <td>117</td>\n",
       "      <td>391</td>\n",
       "      <td>504</td>\n",
       "      <td>909</td>\n",
       "      <td>4</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>437</td>\n",
       "      <td>328</td>\n",
       "      <td>342</td>\n",
       "      <td>250</td>\n",
       "      <td>294</td>\n",
       "      <td>217</td>\n",
       "      <td>84</td>\n",
       "      <td>562</td>\n",
       "      <td>780</td>\n",
       "      <td>633</td>\n",
       "      <td>300</td>\n",
       "      <td>414</td>\n",
       "      <td>82</td>\n",
       "      <td>592</td>\n",
       "      <td>602</td>\n",
       "      <td>861</td>\n",
       "      <td>9</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>445</td>\n",
       "      <td>330</td>\n",
       "      <td>345</td>\n",
       "      <td>220</td>\n",
       "      <td>290</td>\n",
       "      <td>195</td>\n",
       "      <td>128</td>\n",
       "      <td>591</td>\n",
       "      <td>750</td>\n",
       "      <td>526</td>\n",
       "      <td>307</td>\n",
       "      <td>442</td>\n",
       "      <td>111</td>\n",
       "      <td>486</td>\n",
       "      <td>513</td>\n",
       "      <td>882</td>\n",
       "      <td>11</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>334</td>\n",
       "      <td>285</td>\n",
       "      <td>299</td>\n",
       "      <td>128</td>\n",
       "      <td>267</td>\n",
       "      <td>123</td>\n",
       "      <td>185</td>\n",
       "      <td>551</td>\n",
       "      <td>587</td>\n",
       "      <td>532</td>\n",
       "      <td>289</td>\n",
       "      <td>345</td>\n",
       "      <td>251</td>\n",
       "      <td>360</td>\n",
       "      <td>574</td>\n",
       "      <td>902</td>\n",
       "      <td>13</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>423</td>\n",
       "      <td>314</td>\n",
       "      <td>345</td>\n",
       "      <td>276</td>\n",
       "      <td>287</td>\n",
       "      <td>246</td>\n",
       "      <td>281</td>\n",
       "      <td>563</td>\n",
       "      <td>772</td>\n",
       "      <td>647</td>\n",
       "      <td>291</td>\n",
       "      <td>359</td>\n",
       "      <td>145</td>\n",
       "      <td>476</td>\n",
       "      <td>558</td>\n",
       "      <td>854</td>\n",
       "      <td>13</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  Comp-Alexa Fluor 700-A :: CD4  \\\n",
       "0    440    353    319    226    288    201                            119   \n",
       "1    437    328    342    250    294    217                             84   \n",
       "2    445    330    345    220    290    195                            128   \n",
       "3    334    285    299    128    267    123                            185   \n",
       "4    423    314    345    276    287    246                            281   \n",
       "\n",
       "   Comp-BUV737-A :: CD5  Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                   565                                    798   \n",
       "1                   562                                    780   \n",
       "2                   591                                    750   \n",
       "3                   551                                    587   \n",
       "4                   563                                    772   \n",
       "\n",
       "   Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                 580                   287   \n",
       "1                                 633                   300   \n",
       "2                                 526                   307   \n",
       "3                                 532                   289   \n",
       "4                                 647                   291   \n",
       "\n",
       "   Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                            414                 117   \n",
       "1                            414                  82   \n",
       "2                            442                 111   \n",
       "3                            345                 251   \n",
       "4                            359                 145   \n",
       "\n",
       "   Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  Comp-PE-Cy7-A :: CD45RA  \\\n",
       "0                       391                    504                      909   \n",
       "1                       592                    602                      861   \n",
       "2                       486                    513                      882   \n",
       "3                       360                    574                      902   \n",
       "4                       476                    558                      854   \n",
       "\n",
       "   Time :: CD226    class  \n",
       "0              4  CD8_tc0  \n",
       "1              9  CD8_tc0  \n",
       "2             11  CD8_tc0  \n",
       "3             13  CD8_tc0  \n",
       "4             13  CD8_tc0  "
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CD8_tc0_df_grouped = CD8_tc0_df_ungrouped.copy()\n",
    "CD8_tc0_df_grouped[\"class\"] = \"CD8_tc0\"\n",
    "CD8_tc0_df_grouped.to_csv(\"data/CD8_tc0_grouped.csv\", index = False)\n",
    "CD8_tc0_df_grouped.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
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       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
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       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
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       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>0</th>\n",
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       "      <td>316</td>\n",
       "      <td>260</td>\n",
       "      <td>216</td>\n",
       "      <td>285</td>\n",
       "      <td>194</td>\n",
       "      <td>557</td>\n",
       "      <td>734</td>\n",
       "      <td>809</td>\n",
       "      <td>272</td>\n",
       "      <td>378</td>\n",
       "      <td>390</td>\n",
       "      <td>663</td>\n",
       "      <td>510</td>\n",
       "      <td>664</td>\n",
       "      <td>205</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_tcm</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>335</td>\n",
       "      <td>288</td>\n",
       "      <td>298</td>\n",
       "      <td>138</td>\n",
       "      <td>274</td>\n",
       "      <td>129</td>\n",
       "      <td>486</td>\n",
       "      <td>487</td>\n",
       "      <td>807</td>\n",
       "      <td>258</td>\n",
       "      <td>277</td>\n",
       "      <td>307</td>\n",
       "      <td>236</td>\n",
       "      <td>395</td>\n",
       "      <td>523</td>\n",
       "      <td>626</td>\n",
       "      <td>1</td>\n",
       "      <td>CD4_tcm</td>\n",
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       "      <th>2</th>\n",
       "      <td>336</td>\n",
       "      <td>304</td>\n",
       "      <td>283</td>\n",
       "      <td>174</td>\n",
       "      <td>270</td>\n",
       "      <td>165</td>\n",
       "      <td>591</td>\n",
       "      <td>609</td>\n",
       "      <td>806</td>\n",
       "      <td>232</td>\n",
       "      <td>317</td>\n",
       "      <td>389</td>\n",
       "      <td>611</td>\n",
       "      <td>421</td>\n",
       "      <td>500</td>\n",
       "      <td>249</td>\n",
       "      <td>3</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>295</td>\n",
       "      <td>276</td>\n",
       "      <td>274</td>\n",
       "      <td>83</td>\n",
       "      <td>263</td>\n",
       "      <td>81</td>\n",
       "      <td>519</td>\n",
       "      <td>557</td>\n",
       "      <td>638</td>\n",
       "      <td>259</td>\n",
       "      <td>250</td>\n",
       "      <td>282</td>\n",
       "      <td>254</td>\n",
       "      <td>492</td>\n",
       "      <td>466</td>\n",
       "      <td>638</td>\n",
       "      <td>4</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>307</td>\n",
       "      <td>293</td>\n",
       "      <td>268</td>\n",
       "      <td>161</td>\n",
       "      <td>275</td>\n",
       "      <td>150</td>\n",
       "      <td>575</td>\n",
       "      <td>575</td>\n",
       "      <td>792</td>\n",
       "      <td>289</td>\n",
       "      <td>273</td>\n",
       "      <td>386</td>\n",
       "      <td>189</td>\n",
       "      <td>405</td>\n",
       "      <td>583</td>\n",
       "      <td>561</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_tcm</td>\n",
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       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <th>323244</th>\n",
       "      <td>366</td>\n",
       "      <td>278</td>\n",
       "      <td>337</td>\n",
       "      <td>149</td>\n",
       "      <td>262</td>\n",
       "      <td>146</td>\n",
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       "      <td>627</td>\n",
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       "      <td>296</td>\n",
       "      <td>109</td>\n",
       "      <td>568</td>\n",
       "      <td>411</td>\n",
       "      <td>831</td>\n",
       "      <td>1023</td>\n",
       "      <td>CD8_tc0</td>\n",
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       "    <tr>\n",
       "      <th>323245</th>\n",
       "      <td>338</td>\n",
       "      <td>286</td>\n",
       "      <td>303</td>\n",
       "      <td>135</td>\n",
       "      <td>268</td>\n",
       "      <td>129</td>\n",
       "      <td>117</td>\n",
       "      <td>621</td>\n",
       "      <td>24</td>\n",
       "      <td>668</td>\n",
       "      <td>265</td>\n",
       "      <td>294</td>\n",
       "      <td>163</td>\n",
       "      <td>689</td>\n",
       "      <td>398</td>\n",
       "      <td>803</td>\n",
       "      <td>1023</td>\n",
       "      <td>CD8_tc0</td>\n",
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       "    <tr>\n",
       "      <th>323246</th>\n",
       "      <td>340</td>\n",
       "      <td>278</td>\n",
       "      <td>313</td>\n",
       "      <td>121</td>\n",
       "      <td>263</td>\n",
       "      <td>118</td>\n",
       "      <td>52</td>\n",
       "      <td>614</td>\n",
       "      <td>34</td>\n",
       "      <td>597</td>\n",
       "      <td>256</td>\n",
       "      <td>295</td>\n",
       "      <td>130</td>\n",
       "      <td>600</td>\n",
       "      <td>448</td>\n",
       "      <td>831</td>\n",
       "      <td>1023</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>323247</th>\n",
       "      <td>384</td>\n",
       "      <td>280</td>\n",
       "      <td>351</td>\n",
       "      <td>131</td>\n",
       "      <td>261</td>\n",
       "      <td>128</td>\n",
       "      <td>12</td>\n",
       "      <td>621</td>\n",
       "      <td>14</td>\n",
       "      <td>617</td>\n",
       "      <td>281</td>\n",
       "      <td>289</td>\n",
       "      <td>155</td>\n",
       "      <td>607</td>\n",
       "      <td>394</td>\n",
       "      <td>854</td>\n",
       "      <td>1023</td>\n",
       "      <td>CD8_tc0</td>\n",
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       "      <th>323248</th>\n",
       "      <td>336</td>\n",
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       "      <td>149</td>\n",
       "      <td>90</td>\n",
       "      <td>598</td>\n",
       "      <td>30</td>\n",
       "      <td>680</td>\n",
       "      <td>277</td>\n",
       "      <td>285</td>\n",
       "      <td>87</td>\n",
       "      <td>592</td>\n",
       "      <td>451</td>\n",
       "      <td>845</td>\n",
       "      <td>1023</td>\n",
       "      <td>CD8_tc0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2854357 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  \\\n",
       "0         321    316    260    216    285    194   \n",
       "1         335    288    298    138    274    129   \n",
       "2         336    304    283    174    270    165   \n",
       "3         295    276    274     83    263     81   \n",
       "4         307    293    268    161    275    150   \n",
       "...       ...    ...    ...    ...    ...    ...   \n",
       "323244    366    278    337    149    262    146   \n",
       "323245    338    286    303    135    268    129   \n",
       "323246    340    278    313    121    263    118   \n",
       "323247    384    280    351    131    261    128   \n",
       "323248    336    287    300    152    260    149   \n",
       "\n",
       "        Comp-Alexa Fluor 700-A :: CD4  Comp-BUV737-A :: CD5  \\\n",
       "0                                 557                   734   \n",
       "1                                 486                   487   \n",
       "2                                 591                   609   \n",
       "3                                 519                   557   \n",
       "4                                 575                   575   \n",
       "...                               ...                   ...   \n",
       "323244                             73                   572   \n",
       "323245                            117                   621   \n",
       "323246                             52                   614   \n",
       "323247                             12                   621   \n",
       "323248                             90                   598   \n",
       "\n",
       "        Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                                         809   \n",
       "1                                         807   \n",
       "2                                         806   \n",
       "3                                         638   \n",
       "4                                         792   \n",
       "...                                       ...   \n",
       "323244                                     57   \n",
       "323245                                     24   \n",
       "323246                                     34   \n",
       "323247                                     14   \n",
       "323248                                     30   \n",
       "\n",
       "        Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                      272                   378   \n",
       "1                                      258                   277   \n",
       "2                                      232                   317   \n",
       "3                                      259                   250   \n",
       "4                                      289                   273   \n",
       "...                                    ...                   ...   \n",
       "323244                                 627                   268   \n",
       "323245                                 668                   265   \n",
       "323246                                 597                   256   \n",
       "323247                                 617                   281   \n",
       "323248                                 680                   277   \n",
       "\n",
       "        Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                                 390                 663   \n",
       "1                                 307                 236   \n",
       "2                                 389                 611   \n",
       "3                                 282                 254   \n",
       "4                                 386                 189   \n",
       "...                               ...                 ...   \n",
       "323244                            296                 109   \n",
       "323245                            294                 163   \n",
       "323246                            295                 130   \n",
       "323247                            289                 155   \n",
       "323248                            285                  87   \n",
       "\n",
       "        Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  \\\n",
       "0                            510                    664   \n",
       "1                            395                    523   \n",
       "2                            421                    500   \n",
       "3                            492                    466   \n",
       "4                            405                    583   \n",
       "...                          ...                    ...   \n",
       "323244                       568                    411   \n",
       "323245                       689                    398   \n",
       "323246                       600                    448   \n",
       "323247                       607                    394   \n",
       "323248                       592                    451   \n",
       "\n",
       "        Comp-PE-Cy7-A :: CD45RA  Time :: CD226    class  \n",
       "0                           205              0  CD4_tcm  \n",
       "1                           626              1  CD4_tcm  \n",
       "2                           249              3  CD4_tcm  \n",
       "3                           638              4  CD4_tcm  \n",
       "4                           561              5  CD4_tcm  \n",
       "...                         ...            ...      ...  \n",
       "323244                      831           1023  CD8_tc0  \n",
       "323245                      803           1023  CD8_tc0  \n",
       "323246                      831           1023  CD8_tc0  \n",
       "323247                      854           1023  CD8_tc0  \n",
       "323248                      845           1023  CD8_tc0  \n",
       "\n",
       "[2854357 rows x 18 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cells_df = pd.concat([CD4_tcm_df_grouped, CD4_tem_df_grouped, CD4_temra_df_grouped,\n",
    "                    CD4_th0_df_grouped, CD8_tcm_df_grouped, CD8_tem_df_grouped,\n",
    "                    CD8_temra_df_grouped, CD8_tc0_df_grouped])\n",
    "cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>FSC-A</th>\n",
       "      <th>FSC-H</th>\n",
       "      <th>FSC-W</th>\n",
       "      <th>SSC-A</th>\n",
       "      <th>SSC-H</th>\n",
       "      <th>SSC-W</th>\n",
       "      <th>Comp-Alexa Fluor 700-A :: CD4</th>\n",
       "      <th>Comp-BUV737-A :: CD5</th>\n",
       "      <th>Comp-Brilliant Violet 421-A :: CD107a</th>\n",
       "      <th>Comp-Brilliant Violet 605-A :: CD8</th>\n",
       "      <th>Comp-FITC-A :: CD226</th>\n",
       "      <th>Comp-LIVE_DEAD Fixable Blue-A</th>\n",
       "      <th>Comp-PE-A :: TIGIT</th>\n",
       "      <th>Comp-PE-CF594-A :: CD197</th>\n",
       "      <th>Comp-PE-Cy5-A :: CD28</th>\n",
       "      <th>Comp-PE-Cy7-A :: CD45RA</th>\n",
       "      <th>Time :: CD226</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>321</td>\n",
       "      <td>316</td>\n",
       "      <td>260</td>\n",
       "      <td>216</td>\n",
       "      <td>285</td>\n",
       "      <td>194</td>\n",
       "      <td>557</td>\n",
       "      <td>734</td>\n",
       "      <td>809</td>\n",
       "      <td>272</td>\n",
       "      <td>378</td>\n",
       "      <td>390</td>\n",
       "      <td>663</td>\n",
       "      <td>510</td>\n",
       "      <td>664</td>\n",
       "      <td>205</td>\n",
       "      <td>0</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>335</td>\n",
       "      <td>288</td>\n",
       "      <td>298</td>\n",
       "      <td>138</td>\n",
       "      <td>274</td>\n",
       "      <td>129</td>\n",
       "      <td>486</td>\n",
       "      <td>487</td>\n",
       "      <td>807</td>\n",
       "      <td>258</td>\n",
       "      <td>277</td>\n",
       "      <td>307</td>\n",
       "      <td>236</td>\n",
       "      <td>395</td>\n",
       "      <td>523</td>\n",
       "      <td>626</td>\n",
       "      <td>1</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>336</td>\n",
       "      <td>304</td>\n",
       "      <td>283</td>\n",
       "      <td>174</td>\n",
       "      <td>270</td>\n",
       "      <td>165</td>\n",
       "      <td>591</td>\n",
       "      <td>609</td>\n",
       "      <td>806</td>\n",
       "      <td>232</td>\n",
       "      <td>317</td>\n",
       "      <td>389</td>\n",
       "      <td>611</td>\n",
       "      <td>421</td>\n",
       "      <td>500</td>\n",
       "      <td>249</td>\n",
       "      <td>3</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>295</td>\n",
       "      <td>276</td>\n",
       "      <td>274</td>\n",
       "      <td>83</td>\n",
       "      <td>263</td>\n",
       "      <td>81</td>\n",
       "      <td>519</td>\n",
       "      <td>557</td>\n",
       "      <td>638</td>\n",
       "      <td>259</td>\n",
       "      <td>250</td>\n",
       "      <td>282</td>\n",
       "      <td>254</td>\n",
       "      <td>492</td>\n",
       "      <td>466</td>\n",
       "      <td>638</td>\n",
       "      <td>4</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>307</td>\n",
       "      <td>293</td>\n",
       "      <td>268</td>\n",
       "      <td>161</td>\n",
       "      <td>275</td>\n",
       "      <td>150</td>\n",
       "      <td>575</td>\n",
       "      <td>575</td>\n",
       "      <td>792</td>\n",
       "      <td>289</td>\n",
       "      <td>273</td>\n",
       "      <td>386</td>\n",
       "      <td>189</td>\n",
       "      <td>405</td>\n",
       "      <td>583</td>\n",
       "      <td>561</td>\n",
       "      <td>5</td>\n",
       "      <td>CD4_tcm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2039513</th>\n",
       "      <td>393</td>\n",
       "      <td>379</td>\n",
       "      <td>266</td>\n",
       "      <td>308</td>\n",
       "      <td>297</td>\n",
       "      <td>266</td>\n",
       "      <td>321</td>\n",
       "      <td>269</td>\n",
       "      <td>284</td>\n",
       "      <td>296</td>\n",
       "      <td>298</td>\n",
       "      <td>382</td>\n",
       "      <td>249</td>\n",
       "      <td>359</td>\n",
       "      <td>234</td>\n",
       "      <td>333</td>\n",
       "      <td>1023</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2039514</th>\n",
       "      <td>232</td>\n",
       "      <td>273</td>\n",
       "      <td>217</td>\n",
       "      <td>285</td>\n",
       "      <td>265</td>\n",
       "      <td>275</td>\n",
       "      <td>510</td>\n",
       "      <td>363</td>\n",
       "      <td>215</td>\n",
       "      <td>277</td>\n",
       "      <td>273</td>\n",
       "      <td>562</td>\n",
       "      <td>277</td>\n",
       "      <td>216</td>\n",
       "      <td>264</td>\n",
       "      <td>231</td>\n",
       "      <td>1023</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2039515</th>\n",
       "      <td>271</td>\n",
       "      <td>263</td>\n",
       "      <td>265</td>\n",
       "      <td>210</td>\n",
       "      <td>264</td>\n",
       "      <td>203</td>\n",
       "      <td>104</td>\n",
       "      <td>612</td>\n",
       "      <td>67</td>\n",
       "      <td>304</td>\n",
       "      <td>278</td>\n",
       "      <td>500</td>\n",
       "      <td>166</td>\n",
       "      <td>263</td>\n",
       "      <td>294</td>\n",
       "      <td>804</td>\n",
       "      <td>1023</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2039516</th>\n",
       "      <td>280</td>\n",
       "      <td>271</td>\n",
       "      <td>264</td>\n",
       "      <td>170</td>\n",
       "      <td>263</td>\n",
       "      <td>166</td>\n",
       "      <td>237</td>\n",
       "      <td>225</td>\n",
       "      <td>258</td>\n",
       "      <td>251</td>\n",
       "      <td>254</td>\n",
       "      <td>283</td>\n",
       "      <td>242</td>\n",
       "      <td>184</td>\n",
       "      <td>229</td>\n",
       "      <td>221</td>\n",
       "      <td>1023</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2039517</th>\n",
       "      <td>253</td>\n",
       "      <td>261</td>\n",
       "      <td>249</td>\n",
       "      <td>142</td>\n",
       "      <td>259</td>\n",
       "      <td>141</td>\n",
       "      <td>118</td>\n",
       "      <td>612</td>\n",
       "      <td>127</td>\n",
       "      <td>241</td>\n",
       "      <td>249</td>\n",
       "      <td>453</td>\n",
       "      <td>300</td>\n",
       "      <td>227</td>\n",
       "      <td>241</td>\n",
       "      <td>374</td>\n",
       "      <td>1023</td>\n",
       "      <td>debris</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6807430 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         FSC-A  FSC-H  FSC-W  SSC-A  SSC-H  SSC-W  \\\n",
       "0          321    316    260    216    285    194   \n",
       "1          335    288    298    138    274    129   \n",
       "2          336    304    283    174    270    165   \n",
       "3          295    276    274     83    263     81   \n",
       "4          307    293    268    161    275    150   \n",
       "...        ...    ...    ...    ...    ...    ...   \n",
       "2039513    393    379    266    308    297    266   \n",
       "2039514    232    273    217    285    265    275   \n",
       "2039515    271    263    265    210    264    203   \n",
       "2039516    280    271    264    170    263    166   \n",
       "2039517    253    261    249    142    259    141   \n",
       "\n",
       "         Comp-Alexa Fluor 700-A :: CD4  Comp-BUV737-A :: CD5  \\\n",
       "0                                  557                   734   \n",
       "1                                  486                   487   \n",
       "2                                  591                   609   \n",
       "3                                  519                   557   \n",
       "4                                  575                   575   \n",
       "...                                ...                   ...   \n",
       "2039513                            321                   269   \n",
       "2039514                            510                   363   \n",
       "2039515                            104                   612   \n",
       "2039516                            237                   225   \n",
       "2039517                            118                   612   \n",
       "\n",
       "         Comp-Brilliant Violet 421-A :: CD107a  \\\n",
       "0                                          809   \n",
       "1                                          807   \n",
       "2                                          806   \n",
       "3                                          638   \n",
       "4                                          792   \n",
       "...                                        ...   \n",
       "2039513                                    284   \n",
       "2039514                                    215   \n",
       "2039515                                     67   \n",
       "2039516                                    258   \n",
       "2039517                                    127   \n",
       "\n",
       "         Comp-Brilliant Violet 605-A :: CD8  Comp-FITC-A :: CD226  \\\n",
       "0                                       272                   378   \n",
       "1                                       258                   277   \n",
       "2                                       232                   317   \n",
       "3                                       259                   250   \n",
       "4                                       289                   273   \n",
       "...                                     ...                   ...   \n",
       "2039513                                 296                   298   \n",
       "2039514                                 277                   273   \n",
       "2039515                                 304                   278   \n",
       "2039516                                 251                   254   \n",
       "2039517                                 241                   249   \n",
       "\n",
       "         Comp-LIVE_DEAD Fixable Blue-A  Comp-PE-A :: TIGIT  \\\n",
       "0                                  390                 663   \n",
       "1                                  307                 236   \n",
       "2                                  389                 611   \n",
       "3                                  282                 254   \n",
       "4                                  386                 189   \n",
       "...                                ...                 ...   \n",
       "2039513                            382                 249   \n",
       "2039514                            562                 277   \n",
       "2039515                            500                 166   \n",
       "2039516                            283                 242   \n",
       "2039517                            453                 300   \n",
       "\n",
       "         Comp-PE-CF594-A :: CD197  Comp-PE-Cy5-A :: CD28  \\\n",
       "0                             510                    664   \n",
       "1                             395                    523   \n",
       "2                             421                    500   \n",
       "3                             492                    466   \n",
       "4                             405                    583   \n",
       "...                           ...                    ...   \n",
       "2039513                       359                    234   \n",
       "2039514                       216                    264   \n",
       "2039515                       263                    294   \n",
       "2039516                       184                    229   \n",
       "2039517                       227                    241   \n",
       "\n",
       "         Comp-PE-Cy7-A :: CD45RA  Time :: CD226    class  \n",
       "0                            205              0  CD4_tcm  \n",
       "1                            626              1  CD4_tcm  \n",
       "2                            249              3  CD4_tcm  \n",
       "3                            638              4  CD4_tcm  \n",
       "4                            561              5  CD4_tcm  \n",
       "...                          ...            ...      ...  \n",
       "2039513                      333           1023   debris  \n",
       "2039514                      231           1023   debris  \n",
       "2039515                      804           1023   debris  \n",
       "2039516                      221           1023   debris  \n",
       "2039517                      374           1023   debris  \n",
       "\n",
       "[6807430 rows x 18 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "total_df_grouped = pd.concat([cells_df, onlylive_df_grouped, rest_df_grouped])\n",
    "total_df_grouped"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "total_df_grouped.to_csv(\"data/total_grouped.csv\", index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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